That's actually a good point, but the show did answer it in a way already(hand waved really)
Other squads( maybe excluding the nines), so it includes older P13 squad all have the same FranXX model, current squad 13 is the only ones that have those strange individualised ones, leader of P26 said it back in in episode 5.
The question that remains is when were the tests that excluded Naomi conducted and when were the special FranXX built. It seems unreasonable to assume they were built after the tests, but I think we are supposed to assume that or forget it, because otherwise it would mean that somehow Naomi wasn't going to pilot one way or another. It probably is just faulty writing. They wanted to get to the state were Strelizia is they're 5th mecha piloted by 02 and Hiro so they did ignoring everything else.